RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

Searching..................................................done

Query= psy3552
         (92 letters)



>gnl|CDD|202180 pfam02260, FATC, FATC domain.  The FATC domain is named after
          FRAP, ATM, TRRAP C-terminal. The solution structure of
          the FATC domain suggests it plays a role in
          redox-dependent structural and cellular stability.
          Length = 33

 Score = 59.8 bits (146), Expect = 4e-14
 Identities = 18/31 (58%), Positives = 21/31 (67%)

Query: 61 PLSVEGQTKKLIEEATSLDNLCQMYHGWAAY 91
          PLSVE Q  +LI EAT  +NL QMY GW  +
Sbjct: 2  PLSVEQQVDRLISEATDPENLAQMYIGWCPW 32


>gnl|CDD|227365 COG5032, TEL1, Phosphatidylinositol kinase and protein kinases of the
            PI-3 kinase family [Signal transduction mechanisms / Cell
            division and chromosome partitioning / Chromatin
            structure and dynamics / DNA replication, recombination,
            and repair / Intracellular trafficking and secretion].
          Length = 2105

 Score = 45.5 bits (108), Expect = 5e-07
 Identities = 12/47 (25%), Positives = 19/47 (40%)

Query: 46   RLQGKVRSGGQNTTIPLSVEGQTKKLIEEATSLDNLCQMYHGWAAYQ 92
            R + K+        + L +    + LI +AT    L  MY GW  + 
Sbjct: 2059 RFRLKLSEKDAEKFVDLLINKSVESLITQATDPFQLATMYIGWMPFW 2105


>gnl|CDD|233599 TIGR01853, lipid_A_lpxD, UDP-3-O-[3-hydroxymyristoyl] glucosamine
           N-acyltransferase.  This model describes LpxD, an enzyme
           for the biosynthesis of lipid A, a component
           oflipopolysaccharide (LPS) in the outer membrane outer
           leaflet of most Gram-negative bacteria. Some differences
           are found between lipid A of different species. This
           protein represents the third step from
           UDP-N-acetyl-D-glucosamine. The group added at this step
           generally is 14:0(3-OH) (myristate) but may vary; in
           Aquifex it appears to be 16:0(3-OH) (palmitate) [Cell
           envelope, Biosynthesis and degradation of surface
           polysaccharides and lipopolysaccharides].
          Length = 324

 Score = 30.7 bits (70), Expect = 0.063
 Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 2/32 (6%)

Query: 55  GQNTTIPLSVEGQTKKLIEEATSLDNLCQMYH 86
           G NTTI       T  +I E T +DNL Q+ H
Sbjct: 205 GANTTIDRGAFDDT--IIGEGTKIDNLVQIAH 234


>gnl|CDD|223974 COG1044, LpxD, UDP-3-O-[3-hydroxymyristoyl].
          Length = 338

 Score = 29.2 bits (66), Expect = 0.26
 Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 2/33 (6%)

Query: 55  GQNTTIPLSVEGQTKKLIEEATSLDNLCQMYHG 87
           G NTTI       T  +I E   +DNL Q+ H 
Sbjct: 212 GANTTIDRGALDDT--VIGEGVKIDNLVQIGHN 242


>gnl|CDD|234858 PRK00892, lpxD, UDP-3-O-[3-hydroxymyristoyl] glucosamine
           N-acyltransferase; Provisional.
          Length = 343

 Score = 28.6 bits (65), Expect = 0.37
 Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 2/33 (6%)

Query: 55  GQNTTIPLSVEGQTKKLIEEATSLDNLCQMYHG 87
           G NTTI       T  +I E   +DNL Q+ H 
Sbjct: 213 GANTTIDRGALDDT--VIGEGVKIDNLVQIAHN 243


>gnl|CDD|224019 COG1094, COG1094, Predicted RNA-binding protein (contains KH
           domains) [General function prediction only].
          Length = 194

 Score = 25.7 bits (57), Expect = 3.9
 Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 14/37 (37%)

Query: 40  LENIEGRLQGKVRSGGQNTTIPLSVEGQTKKLIEEAT 76
           L  I+GR+ G+              EG+T++ IEE T
Sbjct: 109 LRRIKGRIIGR--------------EGKTRRAIEELT 131


>gnl|CDD|187766 cd09634, Cas1_I-II-III, CRISPR/Cas system-associated protein Cas1. 
           CRISPR (Clustered Regularly Interspaced Short
           Palindromic Repeats) and associated Cas proteins
           comprise a system for heritable host defense by
           prokaryotic cells against phage and other foreign DNA;
           Cas1 is the most universal CRISPR system protein thought
           to be involved in spacer integration; Cas1 is
           metal-dependent deoxyribonuclease, also binds RNA; Shown
           to possess a unique fold consisting of a N-terminal
           beta-strand domain and a C-terminal alpha-helical
           domain.
          Length = 317

 Score = 25.7 bits (57), Expect = 4.1
 Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 1/37 (2%)

Query: 37  KIFLENIEGRLQGKVR-SGGQNTTIPLSVEGQTKKLI 72
           K  +E +E RL+  ++   G+  +    +  Q  KL 
Sbjct: 276 KKLIEALEERLKETIKHYLGRKVSYRRLIRLQAYKLA 312


>gnl|CDD|132519 TIGR03479, DMSO_red_II_alp, DMSO reductase family type II enzyme,
           molybdopterin subunit.  This model represents the
           molybdopterin subunit, typically called the alpha
           subunit, of various proteins that also contain an
           iron-sulfur subunit and a heme b subunit. The group
           includes two distinct but very closely related
           periplasmic proteins of anaerobic respiration, selenate
           reductase and chlorate reductase. Other members of this
           family include dimethyl sulphide dehydrogenase,
           ethylbenzene dehydrogenase, and an archaeal respiratory
           nitrate reductase. This alpha subunit has a
           twin-arginine translocation (TAT) signal for
           Sec-independent translocation across the plasma
           membrane.
          Length = 912

 Score = 25.5 bits (56), Expect = 4.2
 Identities = 8/13 (61%), Positives = 9/13 (69%)

Query: 80  NLCQMYHGWAAYQ 92
             C MYHGW A+Q
Sbjct: 852 GTCIMYHGWEAHQ 864


>gnl|CDD|100043 cd03352, LbH_LpxD, UDP-3-O-acyl-glucosamine N-acyltransferase
           (LpxD): The enzyme catalyzes the transfer of
           3-hydroxymyristic acid or 3-hydroxy-arachidic acid,
           depending on the organism, from the acyl carrier protein
           (ACP) to UDP-3-O-acyl-glucosamine to produce
           UDP-2,3-diacyl-GlcNAc. This constitutes the third step
           in the lipid A biosynthetic pathway in Gram-negative
           bacteria. LpxD is a homotrimer, with each subunit
           consisting of a novel combination of an N-terminal
           uridine-binding domain, a core lipid-binding left-handed
           parallel beta helix (LbH) domain, and a C-terminal
           alpha-helical extension. The LbH domain contains 9
           turns, each containing three imperfect tandem repeats of
           a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X).
          Length = 205

 Score = 25.4 bits (57), Expect = 4.7
 Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 2/33 (6%)

Query: 55  GQNTTIPLSVEGQTKKLIEEATSLDNLCQMYHG 87
           G NTTI     G T  +I + T +DNL Q+ H 
Sbjct: 102 GANTTIDRGALGDT--VIGDGTKIDNLVQIAHN 132


>gnl|CDD|224016 COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope
           biogenesis, outer membrane].
          Length = 281

 Score = 24.9 bits (55), Expect = 7.3
 Identities = 9/20 (45%), Positives = 13/20 (65%)

Query: 57  NTTIPLSVEGQTKKLIEEAT 76
           +T  PL+V G++K   EEA 
Sbjct: 116 DTPNPLNVYGRSKLAGEEAV 135


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.322    0.136    0.403 

Gapped
Lambda     K      H
   0.267   0.0856    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,409,049
Number of extensions: 340702
Number of successful extensions: 222
Number of sequences better than 10.0: 1
Number of HSP's gapped: 222
Number of HSP's successfully gapped: 14
Length of query: 92
Length of database: 10,937,602
Length adjustment: 59
Effective length of query: 33
Effective length of database: 8,320,716
Effective search space: 274583628
Effective search space used: 274583628
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.0 bits)